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The Implications of Over-Estimating Gene Tree Discordance on a Rapid-Radiation Species Tree (Blattodea: Blaberidae)

https://doi.org/10.1101/717660
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Outgoing claims: the papers this work cites, builds on, or argues with.

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Comparison of phylogenetic trees
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Among-site rate variation and its impact on phylogenetic analyses
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Mistranslation-Induced Protein Misfolding as a Dominant Constraint on Coding-Sequence Evolution
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The optimal rate for resolving a near-polytomy in a phylogeny
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Likelihood-based tree reconstruction on a concatenation of aligned sequence data sets can be statistically inconsistent
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Phylogenetic analysis at deep timescales: Unreliable gene trees, bypassed hidden support, and the coalescence/concatalescence conundrum
inferredcites →https://doi.org/10.1016/j.ympev.2015.10.027openalex-snapshot
Implementing and testing the multispecies coalescent model: A valuable paradigm for phylogenomics
inferredcites →https://doi.org/10.1016/j.ympev.2018.05.007openalex-snapshot
Topological support and data quality can only be assessed through multiple tests in reviewing Blattodea phylogeny
inferredcites →https://doi.org/10.1038/nmeth.4285openalex-snapshot
ModelFinder: fast model selection for accurate phylogenetic estimates
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Contentious relationships in phylogenomic studies can be driven by a handful of genes
inferredcites →https://doi.org/10.1073/pnas.1706367114openalex-snapshot
Extensive gene tree discordance and hemiplasy shaped the genomes of North American columnar cacti
inferredcites →https://doi.org/10.1080/03610927808827599openalex-snapshot
Further analysis of the data by Akaike's information criterion and the finite corrections
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An Approximately Unbiased Test of Phylogenetic Tree Selection
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Detecting the Node-Density Artifact in Phylogeny Reconstruction
inferredcites →https://doi.org/10.1080/21686351.1993.12277869openalex-snapshot
Monophylie et Structure Phylogénétique des [Blaberinae + Zetoborinae + Gyninae + Diplopterinae] (Dictyoptera: Blaberidae)
inferredcites →https://doi.org/10.1093/bioinformatics/btg412openalex-snapshot
APE: Analyses of Phylogenetics and Evolution in R language
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STEM: species tree estimation using maximum likelihood for gene trees under coalescence
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phangorn: phylogenetic analysis in R
inferredcites →https://doi.org/10.1093/bioinformatics/btv234openalex-snapshot
ASTRAL-II: coalescent-based species tree estimation with many hundreds of taxa and thousands of genes
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Towards an accurate and efficient heuristic for species/gene tree co-estimation
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Nonlinear Dynamics of Nonsynonymous (dN) and Synonymous (dS) Substitution Rates Affects Inference of Selection
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An Empirical Codon Model for Protein Sequence Evolution
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Mutation-Selection Models of Codon Substitution and Their Use to Estimate Selective Strengths on Codon Usage
inferredcites →https://doi.org/10.1093/molbev/mst192openalex-snapshot
Why Time Matters: Codon Evolution and the Temporal Dynamics of dN/dS
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An Amino Acid Substitution-Selection Model Adjusts Residue Fitness to Improve Phylogenetic Estimation
inferredcites →https://doi.org/10.1093/molbev/msu300openalex-snapshot
IQ-TREE: A Fast and Effective Stochastic Algorithm for Estimating Maximum-Likelihood Phylogenies
inferredcites →https://doi.org/10.1093/molbev/msv003openalex-snapshot
The Relationship between dN/dS and Scaled Selection Coefficients
inferredcites →https://doi.org/10.1093/molbev/msv167openalex-snapshot
Site-Specific Amino Acid Preferences Are Mostly Conserved in Two Closely Related Protein Homologs
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MBE Citation Classics (2018 Edition)
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Transoceanic Dispersal and Plate Tectonics Shaped Global Cockroach Distributions: Evidence from Mitochondrial Phylogenomics
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Species Tree Inference with BPP Using Genomic Sequences and the Multispecies Coalescent
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Coalescent Analysis of Phylogenomic Data Confidently Resolves the Species Relationships in the Anopheles gambiae Species Complex
inferredcites →https://doi.org/10.1093/molbev/msy222openalex-snapshot
Population Genetics Based Phylogenetics Under Stabilizing Selection for an Optimal Amino Acid Sequence: A Nested Modeling Approach
inferredcites →https://doi.org/10.1093/oxfordjournals.molbev.a040153openalex-snapshot
A codon-based model of nucleotide substitution for protein-coding DNA sequences.
inferredcites →https://doi.org/10.1093/oxfordjournals.molbev.a040626openalex-snapshot
Positive Darwinian selection promotes charge profile diversity in the antigen-binding cleft of class I major-histocompatibility-complex molecules.
inferredcites →https://doi.org/10.1093/sysbio/46.3.523openalex-snapshot
Gene Trees in Species Trees
inferredcites →https://doi.org/10.1093/sysbio/syq047openalex-snapshot
Sources of Error Inherent in Species-Tree Estimation: Impact of Mutational and Coalescent Effects on Accuracy and Implications for Choosing among Different Methods
inferredcites →https://doi.org/10.1093/sysbio/syq073openalex-snapshot
The Accuracy of Species Tree Estimation under Simulation: A Comparison of Methods
inferredcites →https://doi.org/10.1093/sysbio/syt057openalex-snapshot
Poor Fit to the Multispecies Coalescent is Widely Detectable in Empirical Data
inferredcites →https://doi.org/10.1093/sysbio/syu085openalex-snapshot
Practical Performance of Tree Comparison Metrics
inferredcites →https://doi.org/10.1093/sysbio/syv029openalex-snapshot
The Challenges of Resolving a Rapid, Recent Radiation: Empirical and Simulated Phylogenomics of Philippine Shrews
inferredcites →https://doi.org/10.1093/sysbio/syv041openalex-snapshot
Can We Identify Genes with Increased Phylogenetic Reliability?
inferredcites →https://doi.org/10.1093/sysbio/syw021openalex-snapshot
RevBayes: Bayesian Phylogenetic Inference Using Graphical Models and an Interactive Model-Specification Language
inferredcites →https://doi.org/10.1093/sysbio/syw119openalex-snapshot
Efficient Bayesian Species Tree Inference under the Multispecies Coalescent
inferredcites →https://doi.org/10.1093/sysbio/syx063openalex-snapshot
Why Concatenation Fails Near the Anomaly Zone
inferredcites →https://doi.org/10.1093/sysbio/syy061openalex-snapshot
Long-Branch Attraction in Species Tree Estimation: Inconsistency of Partitioned Likelihood and Topology-Based Summary Methods
inferredcites →https://doi.org/10.1098/rsbl.2007.0102openalex-snapshot
Death of an order: a comprehensive molecular phylogenetic study confirms that termites are eusocial cockroaches
inferredcites →https://doi.org/10.1098/rspb.2018.2076openalex-snapshot
An integrative phylogenomic approach illuminates the evolutionary history of cockroaches and termites (Blattodea)
inferredcites →https://doi.org/10.1101/601237openalex-snapshot
Phylogenetic Synecdoche Demonstrates Optimality of Subsampling and Improves Recovery of the Blaberoidea Phylogeny
inferredcites →https://doi.org/10.1111/j.1558-5646.2007.00188.xopenalex-snapshot
THE LIKELIHOOD NODE DENSITY EFFECT AND CONSEQUENCES FOR EVOLUTIONARY STUDIES OF MOLECULAR RATES
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The impact of rate heterogeneity on inference of phylogenetic models of trait evolution
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Mojo Hand, a TALEN design tool for genome editing applications
inferredcites →https://doi.org/10.1186/1471-2105-14-348openalex-snapshot
Selecting informative subsets of sparse supermatrices increases the chance to find correct trees
inferredcites →https://doi.org/10.1186/1471-2105-6-134openalex-snapshot
Empirical codon substitution matrix
inferredcites →https://doi.org/10.1186/1471-2148-10-1openalex-snapshot
Genome size differentiates co-occurring populations of the planktonic diatom Ditylum brightwellii(Bacillariophyta)
inferredcites →https://doi.org/10.1186/1471-2148-10-302openalex-snapshot
A maximum pseudo-likelihood approach for estimating species trees under the coalescent model
inferredcites →https://doi.org/10.1186/1471-2148-11-1openalex-snapshot
Phylogenomic reconstruction of lactic acid bacteria: an update
inferredcites →https://doi.org/10.1186/1471-2148-11-369openalex-snapshot
Detecting the symplesiomorphy trap: a multigene phylogenetic analysis of terebelliform annelids
inferredcites →https://doi.org/10.1186/1471-2148-7-1openalex-snapshot
Differential impact of simultaneous migration on coevolving hosts and parasites.
inferredcites →https://doi.org/10.1186/1471-2148-7-147openalex-snapshot
Visualizing differences in phylogenetic information content of alignments and distinction of three classes of long-branch effects
inferredcites →https://doi.org/10.1186/1471-2164-16-s10-s2openalex-snapshot
A comparative study of SVDquartets and other coalescent-based species tree estimation methods
inferredcites →https://doi.org/10.1186/1471-2164-16-s6-s2openalex-snapshot
FunPat: function-based pattern analysis on RNA-seq time series data
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FRESCo: finding regions of excess synonymous constraint in diverse viruses
inferredcites →https://doi.org/10.1371/journal.pcbi.1000501openalex-snapshot
Species Tree Inference by Minimizing Deep Coalescences
inferredcites →https://doi.org/10.1371/journal.pcbi.1000885openalex-snapshot
CodonTest: Modeling Amino Acid Substitution Preferences in Coding Sequences
inferredcites →https://doi.org/10.1371/journal.pgen.1000304openalex-snapshot
The Population Genetics of dN/dS
inferredcites →https://doi.org/10.1371/journal.pone.0036593openalex-snapshot
Long Branch Effects Distort Maximum Likelihood Phylogenies in Simulations Despite Selection of the Correct Model
inferredcites →https://doi.org/10.1371/journal.pone.0130127openalex-snapshot
Phylogeny of Dictyoptera: Dating the Origin of Cockroaches, Praying Mantises and Termites with Molecular Data and Controlled Fossil Evidence
inferredcites →https://doi.org/10.26879/711openalex-snapshot
Fossil calibrations for the cockroach phylogeny (Insecta, Dictyoptera, Blattodea), comments on the use of wings for their identification, and a redescription of the oldest Bla
inferredcites →https://doi.org/10.32614/cran.package.bsdaopenalex-snapshot
BSDA: Basic Statistics and Data Analysis
inferredcites →https://doi.org/10.3389/fgene.2015.00319openalex-snapshot
Trends in substitution models of molecular evolution
inferredcites →https://doi.org/10.5852/ejt.2017.291openalex-snapshot
Molecular phylogeny of Blaberidae (Dictyoptera, Blattodea) with implications for taxonomy and evolutionary studies
inferredcites →https://doi.org/10.7287/peerj.preprints.3489v1openalex-snapshot
Cause of gene tree discord? Distinguishing incomplete lineage sorting and lateral gene transfer in phylogenetics

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inferred← citeshttps://doi.org/10.1101/2020.04.20.049999openalex-snapshot
Disentangling biological and analytical factors that give rise to outlier genes in phylogenomic matrices
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